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What About the Big Y?

At Family Tree DNA’s Conference this past weekend, a new type of DNA test called the Big Y was announced. The test sequences a much larger part of the Y chromosome than done previously by either the standard Y marker (STR) testing, the now defunct Walk the Y(WTY) research program or the Geno 2.0 chip. This test replaces the WTY with much higher coverage and a significantly reduced cost.

Let’s talk for just a minute about those tests.

STR Tests – 12, 25, 37, 67 and 111 Markers

The regular Y marker tests, 12, 25, 37, 67 and 111 were meant to test STR (Short Tandem Repeat) markers for genealogical purposes. This part of the DNA on the Y chromosome repeats itself, like a stutter, and to see if one male matches another male, you count the number of repeats at a particular location. For example, marker 393 often has 13 repeats in haplogroup R. These are used genealogically because they mutate at a faster rate than SNP (Single Nucleotide Polymorphisms) markers. In other words, knowing that you match several thousand people 5000 years ago is not useful genealogically, and that is what you’ve always gotten with SNP markers – haplogroup era information. However, knowing that there are three line defining mutations between your ancestor born in 1683 and you is quite useful genealogically as those line marker mutations serve to identify different lineages within families.

Over the past decade, the Y tree, defined by SNPs, has changed dramatically and significantly. A few years ago, the tree looked much like this…busy, but not overwhelming. Not anymore.

In 2008, the tree was rewritten and dramatically updated. This new tree seemed to be rather permanent, but then came the WTY project and the National Geographic Genographic 2.0 project and the applecart was once again upset. ISOGG currently maintains the most current tree.

WTY (Walk the Y)

The WTY research project was conceptually described in 2007. The goal of the WTY project was to individually examine the DNA of individuals whose STR values were “odd” and out of range enough to cause one to think that perhaps an individual might sport a haplogroup marker previously unknown. Family Tree DNA subsidized this scientific work and new SNPs, which equate to new haplogroup subgroups were indeed discovered. For example, it was through the WTY process in 2010 that we discovered the SNPs that divided the European haplogroup Q males from the Native American haplogroup Q males. In haplogroup Q, that was a watershed event. If you previously took the WTY test, Family Tree DNA will give you a $50 credit towards a Big Y test.

Geno 2.0

In July 2012, the Genographic 2.0 test was introduced. This test takes advantage of chip based sequencing and tests more than 12,000 SNPs on every chip for all participants. This has had the dramatic effect of significantly rearranging the Y tree. For example, on today’s tree, several SNPs by differing names discovered in different labs are considered to be equivalent. Therefore, there is no reason to test all of those SNPs, just one representative SNP, or so we thought.

Well, we were wrong. Because those SNPs weren’t being routinely tested, we never discovered that they weren’t, in fact, always equivalent. This, in combination with many new discoveries, has caused the entire tree to dramatically shift. In fact, how big the shift is really isn’t known yet, but if Miguel Vilar’s and Michael Hammer’s presentations this past weekend are foreshadowing, it’s huge and extends to the root of the European tree itself, haplogroup K, and add extensively to every branch. I’ve seen a prototype of the 2014 tree, and let’s just say, it’s mind-boggling. Virtually every haplogroup name will change, which is why the names are being obsoleted and only SNP number/names remaining, like R-M269 where R indicates the base haplogroup.

Here’s Dr. Hammer rolling out the new scroll that is the new tree and I believe this was only for haplogroup R-M269 (currently R1b1a2). If your eyes just glazed over, mine did too.

The Geno 2.0 test tested more locations than ever before – more than 12,000 SNPs in all. The WTY continued, as did research in other institutions, and addition SNPs have been added that were unknown in late 2011 when the Nat Geo chip was designed.

Comprehensive Y Testing

In response to the genetic genealogy marketplace, in late 2012 or early 2013, Full Genomes Corporation began offering a more comprehensive Y chromosome test. This test was subcontacted to a lab in China and results have been slow in being returned. CeCe Moore provided a “first look” report in early November. In June of 2013, BritainsDNA also began offering a product with coverage slightly greater than that of the Geno 2.0 chip. The one person I have spoken with who has taken both the Full Genomes and Britain’s DNA tests and has results has indicated problems exist with both. Most newly rolled-out products have birthing issues of some sort. He is working with the owners to get the issues resolved.

Debbie Kennett has been attempting to keep the ISOGG testing comparison chart current which is a somewhat daunting task with so few results back yet and many unknown factors.

With Family Tree DNA’s Announcement this weekend of their new Big Y test at an introductory price of $495, sixty percent less than their primary competitor, as one might expect, it has caused a lot of chatter. One advantage that Family Tree DNA has that other companies don’t is that they already own the requisite equipment and they already have the largest Y data base in the world. They will be able to post information to existing clients’ personal pages and projects, for example, and your personal haplotree will be updated. Data will all be in one place. If there is a problem or a change is needed, they don’t have to communicate or negotiate with someone else, someplace else, they can walk just 20 feet down the hallway to check on or to change something in the lab. It’s their lab.

But all of this information begs a very basic question. Why would anyone want to take this test and who does this type of test benefit? It’s estimated that a new SNP occurs about every generation and a half, so there should be a plethora of SNPs waiting to be found.

Who Needs This Test and Why?

This type of test is targeted at males who have one or both situations below.

Has currently taken every available test, meaning through 111 markers and every applicable SNP test for your known haplogroup, and you still need additional information to differentiate lines. Lines, in this context, can mean either family lines or clan lines. With the advent of this new test, some men may want to skip the interim SNP testing and just move directly to this more comprehensive test.

Those who want to learn all they can, participate in and contribute to research. When new SNPs are discovered during the process, which is the goal of the testing, Family Tree DNA has committed to add them to the tree in their proper location immediately. It’s fun to be part of the discovery process and learn something in the process.

Case in Point – Terry Barton

The first SNP that was discovered that was genealogically useful was when Terry Barton was tested several years ago. Initially, this SNP divided the Barton men, but was considered a private SNP because it was not yet found in other surnames. Terry founded the haplogroup R-L196 project. Today, this SNP has been found in the Fowler and Eskew surnames as well, so it is no longer considered a private SNP. The age of this SNP appears to be between 500 and 1000 years and Terry feels that this SNP developed in Lancashire where his ancestors emerged.

With the discovery of family line SNPs, genealogists will be able to use both the regular STR marker tests combined with SNPs to further delineate family groups.

Adoptees and Those Seeking Their Biological Surname

In some cases, the differentiation will be outside of a family line group. For example, let’s say you don’t know your biological surname and you match several men at 67 and 111 markers, none closely, and several distantly. Let’s say that they have also tested currently available SNPs and they all match exactly at the haplogroup level. In this case, I would encourage the adoptee to take the Big Y test and hope that others that you compare against will too. This could be the differentiating factor in determining the biological paternal line when STR markers alone can’t do the job. This will be especially true if the estimate of a new SNP every generation and a half proves to be universally accurate.

The Genealogically or Scientifically Curious

Personally, I want to know as much as I can possibly know about my ancestors. Since I don’t have a Y chromosome, I will be calling my cousin who represents my John R. Estes line and giving this cousin a very nice Christmas gift.

It Might Not Be Useful

I’m sure I don’t have to state the obvious, but I will anyway, you may not discover any private SNPs, but the few results I’ve seen, have all had new SNPs reported. If you do discover a private SNP or SNPs, they may be too far back in time to be genealogically useful. You won’t know if you match others inside or outside of your line unless others test as well. As more people test, these tests will become increasingly useful. The bottom line is this – you’ll never know if you don’t test.

The Price is Right

The BIG Y introductory price is $495 which is, comparatively, a great value. It covers a minimum of 10 million base pairs and approximately 20,000 SNPs. If you previously had the WTY test, your $50 coupon drops the price to $445. These prices hold until December 1st, when the price will revert to $695.

I took the Ancestry.com autosomal test because there are no males willing to be tested. I sent my raw data to FamilyTreeDNA to see what I could learn. Will there be more extensive testing done with my raw data or will I need to take additional tests.
My husband just took the AncestryDNA test, we are waiting for his results. Could you suggest a path of discovery for us?
Thank you for all the great work you are doing. I enjoy reading it all even if I don’t quite understand it yet.

What you are transferring to Family Tree DNA is your raw data results, not your DNA, so they can’t do more testing. You can, however, purchase more tests at FTDNA (like the mtdna, the Y and other trait tests) and they will send you a swab kit.

My suggestion to you would be to contact your matches and see what genealogy you share.

FedMatch has been down for a few days, but when they are again available, you can also transfer your autosomal files there and see what kind of matches you find.

The 1.5 Y-SNPs per generation (other estimates claimed 1 Y-SNP per generation) was based on the hypothetical presumption that the entire 60 mega-bases of the Y-chromosome could be sequenced. This is not the case by any means, and consequently a more realistic expectation should be closer to 1 Y-SNP per every 4 to 6 generations.

…based on the 10 mega-bases reportedly being sequenced by the BIG Y. The discovery rate through Full Genomes Corp., who are able to sequence 20 to 25 mega-bases, appears to be around 1 Y-SNP per 3 to 4 generations, comparatively speaking.

Thank you Vince for clarifying the Y-SNP rate. I’d always wondered where the 1.5 generations figure had come from. I’ve added an update to my blog post: http://cruwys.blogspot.co.uk/2013/11/a-confusion-of-snps.html: I wonder if it will ever be possible to sequence the entire Y-chromosome and, if we do, what we might find..

Roberta,
Do you think the Big Y would be useful when someone has already tested to 67 markers and has just 8 (each one 2-step) matches at the 25 marker level and that’s it for matches? A backbone test given at the time of original testing determined him to be R-M198. I’ve been working with the theory that the reason he has so few matches is that the right people have not tested yet. So would the Big Y help him? (We already have situation 2 covered!) Thanks, Laurie

You know, you just can’t say for sure. You would know more. But unless some of the other people tested too, then it probably wouldn’t be helpful now. However in 6 month or a year when the rest of them are testing, the price will be $695, not $495. Bottom line…it’s up to you.

My brother and I tested. We did not come up as a match to each other or my sisters son. He did match my fathers dna and my oldest son looks so much like my father people at my mothers funeral thought dad came back to life. My aunt gasped wnen she say him. How is it possible we didnt match?. We both did all the tests.Even 111 and family finder. I am H1a1 and my brother is I1.
Has that changed in the last 5 years?

I am tempted to order the Big Y, but I am not sure where it will get me. I am really more interested in more recent ancestry than deep ancestry, but it sounds like this might be a way to find some more recent branchings. Unfortunately to be really helpful I would need some other people to match to.

I think I may be one of those with situation 1. I am J-L26 (J2a4*). If I understand correctly, the * means that I don’t match any of the identified subclades on the FTDNA tree? I have already done the standard Y STR test to 111 markers. I have 16 matches at 67/67, 18 matches at 66/67, and 16 matches at 65/67, and fewer matches at greater differences. I actually have three matches at 111/111, but so far no paper connection. If I understand correctly, this group that might be ideal for the Big Y.

Out of 86 matches at 67 markers, only 11 have upgraded to 111. If so few are willing to upgrade the STR from 67 to 111 I doubt that many will be willing to spend the money for Big Y. But without participation from others I’m not sure what I might accomplish.

This is kind of a chicken and egg situation. It might help you genealogically, if not now, later. If all of you were to test, you’d certainly know a lot more than you do now. If none of you test, everyone waiting for others, then none of you will ever know. If this were me, I’d order it and I’d drop the other men a line telling them why I ordered it. You can always order it later, but the price will certainly be more. It’s one of those personal judgment call situations.

I did go ahead and order the Big Y and now await the results. As I have been looking at some of the information out there I came up with a question, and maybe this isn’t the place for it, but here goes. I’ve read that there can be a SNP on the Y about every 1.7 generations (or something like that). I got to wondering if there is any reason that a SNP could not occur within a STR sequence. For instance, if a STR occurred in the first or last repeat wouldn’t it look the same as if a repeat had dropped out? By the same token, if the STR occurred in the second or the next-to-last repeat it would look like two repeats were dropped. Just a weird thought.

I have been waiting patiently for FTDNA to offer an upgrade to the WTY test that I took when SNP DF13 did not exist! WTY confirmed that I was Z255 and L159.2 derived (+). Being the first of my Beatty name to be reported Z255+ I have been stuck there since whilst the subgroups of other DF13s have expanded crazily! I had already taken the individual L159.2 and then the new Z255 tests before the WTY and as it was limited for my clan no other useful new SNPs were found. With my Big Y test application I hope for new sources of SNP to appear so that I may catch up with my remote DF13 SNP cousins in the New Year. Happy Christmas.
Peter D Beattie R1b-Z255/L159.2+ (Beatty Lineage L-286 (Co. Sligo) Coordinator)

Terry Barton was kind enough to send me an update on the “Barton SNP” situation which I’ve reposted here with his permission. Thanks Terry.

Roberta, I appreciate your great blog and site! I am also pleased that you are your using our Barton terminal SNP as an example. Your statements are pretty close and I’m not sure how important it is to be fully precise – but here are some additional (somewhat rambling) details

1. I don’t claim L196 to be the first genealogically useful SNP (not real sure how to identify first or to define genealogically useful)
a. I don’t recall the surnames – but have heard of a couple of other cases where a terminal SNP is only in one Genetic Group. Dunno who got their SNP first
b. Someone at the 2013 Conference has found two terminal SNPs in their Genetic group – so they have SNP-defined branching within their ySTR defined Group. (hopefully, I can recall who that is)
2. Our Genetic Group has been defined by ySTR matching. Terminal SNP L196 correlates perfectly to the ySTR matching (so far)
3. R-L196 has not been found in any man who we don’t already identify by ySTR as a member of our genetic group (Barton Lineage I) – which does seem to make it a Genetic Group SNP
4. We were included on the ISOGG tree when I reported L196+ results for two Barton Lineage I men with GD=13 at 67 markers. (having L196+ in other surnames of our genetic family did not hurt)
5. We do have 3 other surnames in Barton Lineage I who are tested to be L196+ (Eskew, Fowler & Lucas)
6. All told, we have more than 10 surnames included by ySTR in Barton Lineage I
7. We have not added a single man to Barton Lineage I due to his being L196+

I’m of CF01 in the project, a particularly motivated group. We’re one of only two R1a1a Cooley groups. The MRCA for most (if not all) of us, John Cooley, was born before 1740. Three testers appear to be of a collateral line, although their MRCAs were young enough to have been John’s grandsons.

None of us can afford the Big Y. Apart from the Y-STRs, only one of us has done Geno 2.0 and three of us have done 23andMe. We have the “Young Scandinavian” SNP
(L448) and are negative for CTS4179, the only verified subclade of L448. Additionally, the testers have SNPs that are outside the hierarchy normally expected for an L448 descent. This isn’t surprising and is perhaps expected. Here’s my question–as broad as it is.

Is there any chance that some of these outlying SNPs can be viewed as possible family SNPs. For example, here’s a report I generated for one of the 23andme tests:

I’m, Adrian YP from Surabaya – East Java – Indonesia. Finally, i decided to take an upgrade my Y37 to my Y111 STR’s and BigY (SNP’s) DNA test, the highest resolution Y DNA Testing from an FTDNA Lab because from April 21 – 26 – 2016, FTDNA offered a huge discount for both my Y DNA Testing and i can save about US $123 from the original cost for these most advanced Y DNA Testing i have undertaken at least for today, 2016. I have Y Hg O-CTS5492 and mtDNA Hg B4c (B4c2 from Geno 2,0 DNA Test Results). I know when my both Uniparental DNA Haplogroups were pretty common in Southern Chinese, Austroasiatic and Austronesian population. I can learned more about my deep ancient ancestors with the highest resolution DNA Test to make sure and underline my East and Southeast Asians Heritage from genealogy perspective. I hope i can help an FTDNA Corporation and Lab to learned more about Far East Asians DNA, even though they found when my Y111 STR’s and Y DNA SNP’s aren’t unique at all….., or maybe i have an extremely rare DNA mutations, who knows?…….